Assembly of Phylogenomic Datasets from High-Throughput Sequencing data

Documentation: https://edgardomortiz.github.io/captus.docs

INSTALLATION

Using conda/mamba (recommended)

Captus is available as a conda package. If you have conda or mamba installed, you can easily create a new environment and install Captus with all dependencies using the following command:

conda create -n captus -c bioconda -c conda-forge captus

Warning

Important for macOS users

One of the builds of the latest version of MEGAHIT (v1.2.9) on Bioconda is broken. To ensure you install a functional one, please specify the build number as follows:

conda create -n captus -c bioconda -c conda-forge captus megahit=1.2.9=hfbae3c0_0

Check that Captus was correctly installed:

conda activate captus
captus -h

If the program was correctly installed, you will see the following help message:

usage: captus command [options]

Captus 1.1.0: Assembly of Phylogenomic Datasets from High-Throughput Sequencing data

Captus-assembly commands:
  command     Program commands (in typical order of execution)
                clean = Trim adaptors and quality filter reads with BBTools,
                        run FastQC on the raw and cleaned reads
                assemble = Perform de novo assembly with MEGAHIT and estimate
                           contig depth of coverage with Salmon: Assembling
                           reads that were cleaned with the 'clean' command is
                           recommended, but reads cleaned elsewhere are also
                           allowed
                extract = Recover targeted markers with BLAT and Scipio:
                          Extracting markers from the assembly obtained with
                          the 'assemble' command is recommended, but any other
                          assemblies in FASTA format are also allowed
                align = Align extracted markers across samples with MAFFT or
                        MUSCLE: Marker alignment depends on the directory
                        structure created by the 'extract' command. This step
                        also performs paralog filtering and alignment trimming
                        using ClipKIT

Help:
  -h, --help  Show this help message and exit
  --version   Show Captus' version number

For help on a particular command: captus_assembly command -h

Manual installation

If you are unable to use conda/mamba for any reason, you will need to install all dependencies manually. Please refer to the documentation for details.

USAGE

Documentation and tutorials are available at https://edgardomortiz.github.io/captus.docs

Tip

Extract BUSCO

Since v1.0.1, Captus supports the use of any BUSCO lineage dataset as reference targets for extraction. Just download one of the .tar.gz files from https://busco-data.ezlab.org/v5/data/lineages and provide the path to captus extract.

For example:

captus extract -a 02_assemblies -n ~/Downloads/aves_odb10.2021-02-19.tar.gz

CITATION

Ortiz, E.M., A. Höwener, G. Shigita, M. Raza, O. Maurin, A. Zuntini, F. Forest, W.J. Baker, H. Schaefer. (2023). A novel phylogenomics pipeline reveals complex pattern of reticulate evolution in Cucurbitales. bioRxiv https://doi.org/10.1101/2023.10.27.564367